MBE Advance Access originally published online on April 14, 2004
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Mol. Biol. Evol. 21(7):1455-1458. 2004
DOI: 10.1093/molbev/msh137
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Genome-Scale Phylogeny and the Detection of Systematic Biases
The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
E-mail: matthew.phillips{at}zoo.ox.ac.uk.
Abstract
Phylogenetic inference from sequences can be misled by both sampling (stochastic) error and systematic error (nonhistorical signals where reality differs from our simplified models). A recent study of eight yeast species using 106 concatenated genes from complete genomes showed that even small internal edges of a tree received 100% bootstrap support. This effective negation of stochastic error from large data sets is important, but longer sequences exacerbate the potential for biases (systematic error) to be positively misleading. Indeed, when we analyzed the same data set using minimum evolution optimality criteria, an alternative tree received 100% bootstrap support. We identified a compositional bias as responsible for this inconsistency and showed that it is reduced effectively by coding the nucleotides as purines and pyrimidines (RY-coding), reinforcing the original tree. Thus, a comprehensive exploration of potential systematic biases is still required, even though genome-scale data sets greatly reduce sampling error.
Key Words: genome-scale phylogeny • systematic error • Saccharomyces • RY-coding
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